Methods of processing sample processing devices

ABSTRACT

The methods of the present invention may include some or all of the following activities: providing one or more sample processing devices to a user ( 10 ); collection of sample materials by the user ( 20 ); loading of the sample materials into one or more of the sample processing devices (including, optionally, the loading of reagents with or separate from the sample materials) ( 30 ); sealing of the sample processing devices by the user ( 40 ); forwarding of the loaded sample processing devices to a processing facility by the user ( 50 ); processing of the loaded sample processing devices by the processing facility in accordance with any instructions from the user ( 60 ); providing results of the processing to the user by the processing facility ( 70 ); and destruction, archival, or return of the processed sample processing devices as desired by the user ( 80 ).

RELATED APPLICATIONS

This application claims the benefit under 35 U.S.C. §119(e) of U.S.Provisional Patent Application Ser. No. 60/344,857 filed on 31 Dec.2001, which is hereby incorporated by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to the field of sample processing devices.More preferably, the present invention relates to the processing ofsample processing devices.

BACKGROUND

The development of methods and techniques for analysis of genomic andproteomic biological materials provides powerful tools for clinicalpractitioners as well as medical practitioners. In many instances,however, the expertise and/or the equipment required to practice thesemethods and techniques is not available in a clinical setting. Forexample, the skill and equipment required to perform a DNA sequencinganalysis is simply beyond the skills of a vast majority of clinicalpractitioners. Furthermore, access to personnel and/or facilities thatcan perform such analyses is also typically limited.

What is needed is a method that allows the clinical practitioner orother unskilled users access to the advanced methods and techniques ofgenomic and proteomic analysis of biological materials in a convenient,cost-effective and timely manner.

SUMMARY OF THE INVENTION

The present invention provides methods of using sample processingdevices to process sample materials. The methods of the presentinvention provide users with the ability to obtain advanced processingof sample materials while not requiring the user to obtain the skills orthe equipment required to perform the desired analyses. In otherinstances, the methods of the present invention can offer users theability to focus their efforts on other activities.

The present invention takes advantage of recent advances in sampleprocessing devices, especially in disposable sample processing devicesthat can be used to perform, e.g., genomic analyses such as polymerasechain reaction (PCR), Sanger sequencing, etc.

Furthermore, the sealed nature of the sample processing devices used inconnection with the present invention provides advantages because inmany instances the sample materials are not transferred betweencontainers or devices during processing, instead remaining within theconfines of the sample processing devices into which they were loaded bythe user. That sealed nature may, for example, provide protection byreducing the likelihood that viruses or other pathogens included in thesample materials can escape from the sample processing devices. Inaddition, many, if not all, of the processes performed on the samplematerials loaded in the sample processing devices are automated.Automation can be useful in reducing the variability inherent in manualprocesses, it may also provide additional control overcross-contamination of sample materials contained in other sampleprocessing devices.

In one aspect, the methods of the present invention include some or allof the following activities: providing one or more sample processingdevices to a user; collection of sample materials by the user; loadingof the sample materials into one or more of the sample processingdevices (including, optionally, the loading of reagents with or separatefrom the sample materials); sealing of the sample processing devices bythe user; forwarding of the loaded sample processing devices to aprocessing facility by the user; processing of the loaded sampleprocessing devices by the processing facility in accordance with anyinstructions from the user; providing results of the processing to theuser by the processing facility; and destruction, archival, or return ofthe processed sample processing devices as desired by the user.

In other aspects, the present invention may provide a method of using asample processing device, the method including loading biological samplematerial into a sample processing device by a user; sealing of thebiological sample material in the sample processing device; shipping thesample processing device to a processing facility after sealing thesample processing device; processing the biological sample material inthe sample processing device at the processing facility; andcommunicating results of the processing to the user.

In various other embodiments, the methods may also involve loading areagent into the sample processing device before sealing of the sampleprocessing device by the user and/or loading a reagent into the sealedsample processing device at the processing facility.

The methods may optionally include processing the biological samplematerial by performing genomic analysis of the biological samplematerial; performing polymerase chain reaction processing of thebiological sample material; performing Sanger sequencing processing ofthe biological sample material; performing electrophoretic separation,etc.

The methods may further include archiving of the sample process devicecontaining the biological sample material after processing thebiological sample material at the processing facility and communicatingthe results to the user.

The methods may also include shipping the sample process devicecontaining the biological sample material to the user after processingthe biological sample material at the processing facility.

Optionally, the methods of the present invention may include collectionof the biological sample material by the user before loading the sampleprocessing device with the biological sample material. In anotheroption, the method may include collection of the biological samplematerial by the user and combining of a reagent with the biologicalsample material before loading the biological sample material into thesample processing device.

In still other methods, the sealing may include placing a tamper-evidentseal on the sample processing device and/or placing a seal includingpressure sensitive adhesive on the sample processing device.

These and other features and advantages of the invention may bedescribed below in connection with illustrative embodiments of theinvention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a flow diagram of one illustrative method of the presentinvention.

DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS OF THE INVENTION

The sample processing devices used in connection with the methods of thepresent invention may preferably be designed for processing samplematerials that include biological material such as peptide- and/ornucleotide-containing material. Examples of some sample processingdevices and methods of using them that may be used in connection withthe methods of the present invention include those devices described in,e.g., commonly-assigned U.S. patent application Ser. No. 09/894,810,filed on Jun. 28, 2001 and entitled ENHANCED SAMPLE PROCESSING DEVICESSYSTEMS AND METHODS and U.S. patent application Ser. No. 09/895,010,filed on Jun. 28, 2001 and entitled SAMPLE PROCESSING DEVICES. Otheruseable device constructions may be found in, e.g., U.S. ProvisionalPatent Application Ser. No. 60/214,508 filed on Jun. 28, 2000 andentitled THERMAL PROCESSING DEVICES AND METHODS; U.S. Provisional PatentApplication Ser. No. 60/214,642 filed on Jun. 28, 2000 and entitledSAMPLE PROCESSING DEVICES, SYSTEMS AND METHODS; U.S. Provisional PatentApplication Ser. No. 60/237,072 filed on Oct. 2, 2000 and entitledSAMPLE PROCESSING DEVICES, SYSTEMS AND METHODS; U.S. Provisional PatentApplication Ser. No. 60/260,063 filed on Jan. 6, 2001 and entitledSAMPLE PROCESSING DEVICES, SYSTEMS AND METHODS; U.S. Provisional PatentApplication Ser. No. 60/284,637 filed on Apr. 18, 2001 and entitledENHANCED SAMPLE PROCESSING DEVICES, SYSTEMS AND METHODS; U.S. patentapplication Ser. No. 09/837,073, filed on Apr. 18, 2001 and entitledMULTI-FORMAT SAMPLE PROCESSING DEVICES, METHODS AND SYSTEMS (AttorneyDocket No. 56545USA4A.003); and U.S. Patent Application Publication No.US 2002/0048533 A1 filed Jun. 28, 2001 and entitled SAMPLE PROCESSINGDEVICES AND CARRIERS. Additional clean-up and/or removal materials andother features may be found in, e.g., U.S. patent application Ser. No.10/027,226 filed Dec. 20, 2001 and entitled METHODS AND DEVICES FORREMOVAL OF ORGANIC MOLECULES FROM BIOLOGICAL MIXTURES USING AHYDROPHILIC SOLID SUPPORT IN A HYDROPHOBIC MATRIX (Attorney Docket No.57313US002) and in U.S. patent application Ser. No. 10/027,222 filedDec. 20, 2001 and entitled METHODS AND DEVICES FOR REMOVAL OF ORGANICMOLECULES FROM BIOLOGICAL MIXTURES USING ANION EXCHANGE (Attorney DocketNo. 57314US002). Other devices and methods are described in U.S. patentapplication Ser. No. 10/034,334 filed Dec. 28, 2001 and entitled SAMPLEPROCESSING DEVICE WITH INTEGRAL ELECTROPHORETIC CHANNELS (AttorneyDocket No. 56544US002).

In addition to the devices described in these commonly-assigned patentapplications, the methods of the present invention may also be performedusing other devices and processing methods. Examples of some suitablesample processing devices may be described in, e.g., InternationalPublication Nos. WO 97/36681 (Woudenberg et al.); WO 98/22625 (Burns etal.); WO 98/45481 (Knapp et al.); WO 99/43432 (Dubrow et al.); WO00/05582 (Virtanen); WO 00/40750 (Orlefors et al.); WO 01/47638 (Tookeet al.); as well as in U.S. Pat. No. 5,229,297 (Schnipelsky et al.);U.S. Pat. No. 5,304,487 (Wilding et al.); U.S. Pat. No. 5,585,069(Zanzucchi et al.); U.S. Pat. No. 5,587,128 (Wilding et al.); U.S. Pat.No. 5,639,428 (Cottingham); U.S. Pat. No. 6,030,581 (Virtanen); U.S.Pat. No. 6,126,899 (Woudenberg et al.); U.S. Pat. No. 6,123,798 (Gandhiet al.); and U.S. Pat. No. 6,319,469 B1 (Mian et al.).

FIG. 1 is a flow diagram of one illustrative method according to thepresent invention. It will be understood that the depicted method isillustrative in nature only and includes a number of optional steps thatmay or may not be included within the scope of the present invention asit may be most broadly defined.

The initial step 10 in the flow chart includes providing one or moresample processing devices to a user for receiving sample materials. Thesample processing devices may, e.g., be manufactured according to theprinciples and teachings of any of the above-identified patentdocuments. Further, the user may be supplied with different sampleprocessing devices so that they have the opportunity to select thedevice or devices most appropriate for the analyses they desire to haveperformed. Further, the sample processing devices may be preloaded withvarious reagents or other materials as discussed in many of theabove-identified patent documents.

The next step 20 in the depicted method involves collection of a samplecontaining biological material by the user. The sample may be obtainedby any suitable technique and may constitute any type of biologicalmaterial (as described above). Examples of some exemplary samplescontaining biological material include blood, etc. Depending on thecapabilities of the sample processing devices into which the sample isto be loaded, the actual collected sample may be processed by the userinto a form appropriate for analysis on the sample processing device.For example, it may be desirable to combine the sample with a desiredreagent or reagents (e.g., PCR primers, etc.). In other instances, itmay be desirable for the user to perform additional pre-loadingprocesses to put the sample into shape for analysis on the sampleprocessing device.

After collecting the sample material, the next step 30 in the depictedmethod involves loading of the sample material into one or more of thesample processing devices. The loading may be performed into more thanone sample processing device where, e.g., different analyses are desiredthat are performed on different sample processing devices, verificationof the integrity of the results is desired (by providing redundanttesting on different sample processing devices), etc. The loading may beaccomplished by hand or by automated processes and equipment (or acombination of both). Furthermore, the loading of sample materials maybe accompanied by loading of reagents (e.g., PCR primers, etc.) into thesame or different chambers on the sample processing devices.

After loading the sample processing devices, the next step 40 includessealing of the sample processing device by the user to prevent leakage,evaporation, and/or cross-contamination between different sampleprocessing devices. The seals may preferably be tamper-evident to ensureintegrity of the results. Any suitable sealing techniques may be usedalthough it may be preferred to use a pressure-sensitive adhesive coatedcover tape for ease of use.

If a pressure sensitive adhesive seal is to be used, it may be preferredthat the pressure sensitive adhesive be disposed on a backing(preferably, a backing that is transparent to electromagnetic energy ofselected wavelengths). The adhesive is preferably selected such that itadheres well to materials of which the sample processing devices aremade (e.g., polyolefins, polystyrene, polycarbonate, or combinationsthereof), maintains adhesion during high and low temperature storage(e.g., about −80° C. to about 150° C.) while providing an effective sealagainst sample evaporation, does not substantially dissolve in orotherwise react with the components of the sample materials or reagents.Thus, the type of adhesive is not critical as long as it does notinterfere (e.g., bind DNA, dissolve, etc.) with any processes performedin the sample processing device. Preferred adhesives include thosetypically used on cover films of analytical devices in which biologicalreactions are carried out. These include poly-alpha olefins andsilicones, for example, as described in International Publication Nos.WO 00/45180 (Ko et al.) and WO 00/68336 (Ko et al.).

Following sealing of the sample processing device, the next step 50 inthe method involves forwarding of the loaded sample processing devicesto a processing facility that has the equipment and personnel requiredto perform the desired analyses on the sample materials loaded into thesample processing devices. The sample processing devices may be shippedor transported by any suitable carrier, e.g. courier, mail, etc. Theloaded sample processing devices may be packaged in any suitablecontainer depending on the nature of the sample materials, therequirements of the carrier, etc.

Upon receipt of the loaded sample processing devices, the next step 60in the method involves processing of the loaded sample processingdevices by the processing facility according to the instructionsreceived from the user and/or the nature of the sample processingdevices. Examples of some suitable processes that may be performedinclude, e.g., PCR amplification, Sanger sequencing, electrophoreticseparations, etc. The processing may include the introduction of one ormore desired reagents into the sample processing devices at theprocessing facility. This may be useful where, e.g., reagents areunavailable to the user who loaded the sample materials into the sampleprocessing devices, the reagents are not stable enough to withstandshipment, etc.

After processing in the processing facility, the next step 70 involvescommunicating the results of the various analyses to the user who loadedthe sample processing devices and provided them to the processingfacility. Communication of the test results to the user may be by anysuitable technique, e.g., voice (e.g., telephone), in person, mail,electronic mail, Internet-based communication, etc. The informationcommunicated may include images and/or other information in addition toor in place of alpha-numeric data.

Another optional step 80 in the depicted method involves handling of thesample processing devices after processing by the processing facility.In some instances, the user may request that the sample processingdevices be destroyed after processing and collection of the datagenerated as a result of the processing. In other instances, the usermay request that the processing facility retain and archive the sampleprocessing devices to allow for, e.g., later verification of the resultsof the processing. In other instances, the user may request that thesample processing devices be returned after processing, with the userarranging for destruction or archiving of the processed devices.

Patents, patent applications, and publications disclosed herein arehereby incorporated by reference (in their entirety) as if individuallyincorporated. It is to be understood that the above description isintended to be illustrative, and not restrictive. Various modificationsand alterations of this invention will become apparent to those skilledin the art from the foregoing description without departing from thescope of this invention, and it should be understood that this inventionis not to be unduly limited to the illustrative embodiments set forthherein.

1. A method of using a sample processing device, the method comprising:loading biological sample material into a sample processing device by auser; sealing of the biological sample material in the sample processingdevice; shipping the sample processing device to a processing facilityafter sealing the sample processing device; processing the biologicalsample material in the sample processing device at the processingfacility; and communicating results of the processing to the user.
 2. Amethod according to claim 1, further comprising loading a reagent intothe sample processing device before sealing of the sample processingdevice by the user.
 3. A method according to claim 1, further comprisingloading a reagent into the sealed sample processing device at theprocessing facility.
 4. A method according to claim 1, whereinprocessing the biological sample material comprises genomic analysis ofthe biological sample material.
 5. A method according to claim 1,wherein processing the biological sample material comprises polymerasechain reaction processing of the biological sample material.
 6. A methodaccording to claim 1, wherein processing the biological sample materialcomprises Sanger sequencing processing of the biological samplematerial.
 7. A method according to claim 1, wherein processing thebiological sample material comprises electrophoretic separation.
 8. Amethod according to claim 1, further comprising archiving of the sampleprocess device containing the biological sample material afterprocessing the biological sample material at the processing facility andcommunicating the results to the user.
 9. A method according to claim 1,further comprising shipping the sample process device containing thebiological sample material to the user after processing the biologicalsample material at the processing facility.
 10. A method according toclaim 1, further comprising collection of the biological sample materialby the user before loading the sample processing device with thebiological sample material.
 11. A method according to claim 1, furthercomprising collection of the biological sample material by the user andcombining of a reagent with the biological sample material beforeloading the biological sample material into the sample processingdevice.
 12. A method according to claim 1, wherein the sealing comprisesplacing a tamper-evident seal on the sample processing device.
 13. Amethod according to claim 1, wherein the sealing comprises placing aseal that comprises pressure sensitive adhesive on the sample processingdevice.